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Mol. Cells 2014; 37(11): 795-803

Published online November 30, 2014

https://doi.org/10.14348/molcells.2014.0127

© The Korean Society for Molecular and Cellular Biology

Antagonistic Regulation of Arabidopsis Growth by Brassinosteroids and Abiotic Stresses

Yuhee Chung1,4, Soon Il Kwon2, and Sunghwa Choe1,2,3,*

1School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea, 2Convergence Research Center for Functional Plant Products, Advanced Institutes of Convergence Technology, Suwon 443-270, Korea, 3Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea, 4Present address: Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, USA

Correspondence to : *Correspondence: shchoe@snu.ac.kr

Received: May 15, 2014; Revised: September 6, 2014; Accepted: September 11, 2014

To withstand ever-changing environmental stresses, plants are equipped with phytohormone-mediated stress resistance mechanisms. Salt stress triggers abscisic acid (ABA) signaling, which enhances stress tolerance at the expense of growth. ABA is thought to inhibit the action of growth-promoting hormones, including brassinosteroids (BRs). However, the regulatory mechanisms that coordinate ABA and BR activity remain to be discovered. We noticed that ABA-treated seedlings exhibited small, round leaves and short roots, a phenotype that is characteristic of the BR signaling mutant, brassinosteroid insensitive1-9 (bri1-9). To identify genes that are antagonistically regulated by ABA and BRs, we examined published Arabidopsis microarray data sets. Of the list of genes identified, those upregulated by ABA but downregulated by BRs were enriched with a BRRE motif in their promoter sequences. After validating the microarray data using quantitative RT-PCR, we focused on RD26, which is induced by salt stress. Histochemical analysis of transgenic Arabidopsis plants expressing RD26pro:GUS revealed that the induction of GUS expression after NaCl treatment was suppressed by co-treatment with BRs, but enhanced by co-treatment with propiconazole, a BR biosynthetic inhibitor. Similarly, treatment with bikinin, an inhibitor of BIN2 kinase, not only inhibited RD26 expression, but also reduced the survival rate of the plant following exposure to salt stress. Our results suggest that ABA and BRs act antagonistically on their target genes at or after the BIN2 step in BR signaling pathways, and suggest a mechanism by which plants fine-tune their growth, particularly when stress responses and growth compete for resources.

Keywords ABA, abiotic stress, BIN2, brassinosteroids, RD26, Root

Due to their sessile nature, plants have developed strategies to cope with abiotic challenges and biotic stresses (Chung et al., 2012; Kim et al., 2014; Maharjan and Choe, 2011). Plants exposed to abiotic stresses display severe growth retardation and reduced productivity. Growth is regulated by plant hormones, which modify endogenous programs in response to exogenous signals. However, the hormone-dependent mechanisms by which growth is inhibited under stress conditions are not fully understood. The molecular mechanisms that impart tolerance to water stress can be divided into abscisic acid (ABA)-dependent and ABA-independent pathways (Shinozaki and Yamaguchi-Shinozaki, 2007). ABA plays vital roles in adaptation to environmental changes, seed dormancy, and the regulation of stomatal closure (Grill and Himmelbach, 1998; Lee and Luan, 2012).

Under stressed conditions, plants rapidly produce ABA, which stimulates the resistance mechanism. In the ABA-dependent pathway, ABA binds to soluble receptors of the PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS (RCARs) family, which induces the de novo synthesis of ABA through 9-cis epoxycarotenoid dioxygenase (NCED) as part of a positive feedback mechanism (Ma et al., 2009; Park et al., 2009). Once ABA activates SnRK2s, SnRK2s phosphorylate and thereby activate the transcription of ABA-dependent transcription factors, such as ABA-responsive element binding factors (ABFs/AREBs) (Furihata et al., 2006; Uno et al., 2000). ABFs/AREBs then bind to the ABA response element (ABRE) in the promoter region of their target genes (Mundy et al., 1990). These conserved elements contain PyACGTGGC (Busk and Pages, 1997; Guiltinan et al., 1990; Yamaguchi-Shinozaki et al., 1990) and ACGTG[G/T]C (Hobo et al., 1999) residues. ABA regulates approximately 10% of the genes in Arabidopsis, and many of these genes are also regulated by other hormones (Nemhauser et al., 2006).

In addition to ABFs/AREBs, other ABA-induced transcription factors are known to participate in the ABA response and stress tolerance. For instance, the NAC (NAM, ATAF1/2 and CUC2) transcription factor family, which largely consists of NO APICAL MERISTEM (NAM) and Arabidopsis thaliana transcription activation factor (ATAF1/2) transcription factors, is known to function in the stress response (Aida et al., 1997). ATAF1/ANAC002 directly regulates ABA biosynthesis through the transcriptional activation of NCED3 (Jensen et al., 2013; Tran et al., 2004). RD26 is a member of the ATAF family and is reported to function in ABA-dependent stress-response pathways (Fujita et al., 2004; Ooka et al., 2003).

Brassinosteroids (BRs) are a class of plant steroidal hormones (Chung and Choe, 2013). Like mammalian steroid hormones such as estrogen, ecdysone, and progesterone, BRs play key roles in plant development, regulating processes such as cell elongation, vascular system differentiation, senescence, and stress responses (Choe, 2006; Clouse and Sasse, 1998). BRs and other phytohormones have numerous target genes in common, and complex crosstalk mechanisms exist among these hormone signal transduction pathways (Chung et al., 2011; Nemhauser et al., 2006). Brassinolide (BL), the most active form of BRs, binds to an island domain in the extracellular domain of BRASSINOSTEROID INSENSITIVE 1 (BRI1) (Kinoshita et al., 2005; Sun et al., 2013). In the absence of BL, BKI1 binds to the cytoplasmic kinase domain of BRI1 and thereby inhibits its phosphorylation function (Wang et al., 2008). However, when BL binds to BRI1, BKI1 is released from BRI1 and BRI1 forms a heterodimer with BRI1-ASSOCIATED-KINASE 1 (BAK1) (Russinova et al., 2004; Wang and Chory, 2006). Then, BR-SIGNALING KINASE 1 (BSK1) is released from the cytoplasmic domain of BRI1 and transduces the signal into the nucleus via a protein phosphatase, bri1 SUPPRESSOR1 (BSU1) (Kim et al., 2009; Tang et al., 2008). BSU1 inactivates the BR-INSENSITIVE 2 (BIN2) kinase that acts as a negative regulator in BR signaling pathways (Choe et al., 2002; Li and Nam, 2002; Li et al., 2001). BIN2 negatively regulates BR-specific transcription factors, including BZR1 and BES1 by phosphorylation (Kim et al., 2009), and is degraded in response to BL (Peng et al., 2008). BZR1 binds to the BR response element (BRRE) motif (CGTG[T/C][G/A]) (He et al., 2005) to both activate BR response genes and inhibit BR biosynthetic genes, including DWF4 (Choe et al., 2001; Kim et al., 2006; 2013). Weak alleles of bri1 include bri1-5 (Noguchi et al., 1999) and bri1-9, and exhibits a semi-dwarf phenotype (Jin et al., 2007).

In contrast to the ABA pathway, the majority of signaling components have been elucidated in the BR signaling cascade (Vriet et al., 2013). Given the importance of ABA and BRs, much research has focused on identifying the mechanism of crosstalk between BRs and ABA. It has been demonstrated that ABA and BRs antagonistically regulate each other during seed germination and root growth inhibition (Steber and McCourt, 2001; Zhang et al., 2009)

In this study, we sought to understand the mechanisms by which BRs and ABA interact. First, we selected putative marker genes that are antagonistically regulated by BRs and ABA from a microarray database deposited in AtGenExpress (Nemhauser et al., 2006). Secondly, we found that chemical inhibition of BIN2 decreased the plant’s tolerance to salt stress, suggesting that BIN2 is involved in ABA-mediated salt tolerance processes. Based on our findings, we propose a model in which transcription factors that bind to common target genes and are specific to either BRs or ABA are antagonistically regulated by each other to bring about ABA-dependent stress responses.

Plant material and growth conditions

Arabidopsis plants of Columbia ecotype were grown in 0.5×Murashige and Skoog (MS) medium containing 0.5% sucrose and 0.8% plant agar. Plants or seedlings were kept in a growth room at 22°C with a 16 h light/8 h dark cycle. To measure the survival rate in salt media, seeds were germinated and grown in MS agar medium and transferred to medium containing the indicated concentrations of hormone or chemical. After 1 day, seedlings were transferred again to medium containing NaCl. epi-Brassinolide (BL) was dissolved in DMSO, and ABA stock was prepared in ethyl alcohol (EtOH). The controls contained the same volume of DMSO or EtOH as chemicals added to the treated aliquots, and considered a mock treatment.

Quantitative RT-PCR

RNA extraction and cDNA synthesis were conducted according to a previous report (Chung et al., 2012). Quantitative RT-PCR analysis was performed using SYBR-mix (KAPA Biosystems). UBQ10 was used as an internal control. Primer sets used for PCR are listed in Supplementary Table S2.

GUS histochemical assay and quantification of GUS activity

Five-day-old RD26pro:GUS transgenic seedlings were first treated with the indicated concentrations of hormone or chemical. Following pre-incubation, each seedling was transferred to NaCl-containing agar medium supplemented with the same concentration of hormone or chemical. After 3 days, seedlings were transferred to GUS buffer (1 mM 5-bromo-4-chloro-3-indoyl-β-d-GlcUA, 100 mM sodium phosphate (pH 7), 5 mM potassium ferrocyanide, 5 mM potassium ferricyanide, 10 mM EDTA, and 0.1% (v/v) Triton X-100) and incubated for 2 h. Serially-diluted EtOH was used to clear the chloroplasts and to reduce background staining. Micrographs were taken using a stereomicroscope (Olympus). To quantify the in vivo GUS activity of RD26pro:GUS in each treatment, 0.5 cm of the root tip of treated seedlings was excised and transferred to 96-well plates pre-filled with a substrate solution (Blazquez et al., 1998). Seedlings in the substrate solution were incubated for 1 h at 37°C and the reaction was stopped by the addition of 100 μl of cold 0.2 M Na2CO3 solution. The fluorescence intensity was measured using a fluorescence spectrophotometer (Varian, USA) with an excitation wavelength of 360 nm and an emission wavelength of 465 nm. The values of 12 seedlings were averaged and plotted with their standard error. The standard curve was calculated using known concentrations of 4-methylumbelliferol solution.

Motif prediction by MEME

MEME (http://meme.sdsc.edu) was used to search for motifs conserved in the promoter region 1000 bp upstream of the start codons of genes antagonistically regulated by ABA and BR (Bailey and Elkan, 1995). A MEME search revealed that the optimum width for motifs was 6 to 9 bp.

Morphological similarity between ABA-treated seedlings and the BR-deficient dwarf mutant

We observed that treatment of Arabidopsis seedlings with ABA often resulted in phenotypes that resembled those of BR-deficient dwarf mutants. The small, curled leaves of ABA-treated Col wild-type plants were similar to those of mock-treated bri1-9 plants (Figs. 1A and 1B), which bear a loss-of-function mutation in the BR receptor (Jin et al., 2007). Previously, we also showed that BR mutants are more sensitive to ABA treatment (Choe et al., 2002). These findings suggest that ABA and BRs interact to regulate Arabidopsis growth.

Because ABA treatment mimicked the BR mutant phenotype, we reasoned that bri1-9 would be more sensitive to ABA than the wild type. To test this, we performed a dose-response assay in which we examined the key characteristics of seedling development, including root growth, germination, and post-germination growth, under various concentrations of ABA. The root growth rate of wild-type plants was reduced in response to ABA treatment in a dose-dependent manner, and the degree of reduction was much greater in bri1-9 (Fig. 1C). In addition, we scored the percentage of seeds with emerged radicles 3 days after sowing on mock, 0.4, 0.8, and 1.2 μM ABA medium (Fig. 1D). On 0.8 μM ABA, 80% of the Col seeds germinated, whereas only 25% of bri1-9 seeds did, suggesting that bri1-9 is more sensitive to exogenous ABA treatment than is the wild type (Fig. 1E). Of the germinated seeds, only 55% and 19% of the cotyledons of wild-type and bri1-9 seedlings remained green, respectively, at 0.8 μM ABA (Fig. 1F). Thus, the growth of bri1-9 plants was more sensitive to ABA than the wild type, suggesting that ABA controls BR signaling pathways to achieve optimal growth and development during the ABA-mediated stress response.

BRs and ABA antagonistically regulate overlapping sets of genes

To identify the genes that are oppositely regulated by ABA and BRs, we analyzed a set of publicly available microarray data that were reported by Nemhauser et al. (2006). They reported that 383 genes upregulated by BRs, 268 were downregulated by BRs, 1440 were upregulated by ABA, and 1476 were downregulated by ABA (Nemhauser et al., 2006). Because BRs and ABA have a tendency to reverse the effects on Arabidopsis growth (Fig. 1), we focused on genes that respond oppositely to BRs and ABA. We determined the union (62) of genes downregulated by BRs and upregulated by ABA, and the union (50) upregulated by BRs and downregulated by ABA (Fig. 2A). These genes were chosen for further investigation.

Because BZR1 can function either as an inducer or repressor of BR-responsive genes (He et al., 2005), we determined the number of BR-response elements (BRREs, CGTG[TC][GA], (He et al., 2005)) in the promoter DNA sequences of these genes (Fig. 2B). Whereas 25% of genes in the whole genome contained the BRRE motif, 48% of genes upregulated by ABA and downregulated by BR contained this motif (Fig. 2B). Since the BRRE was not enriched in the group of genes downregulated by ABA and upregulated by BR, we propose that genes that are upregulated by ABA and downregulated by BR are likely targeted by BZR1 through direct binding to BRRE in the promoter sequences.

We next determined the frequency of the BRRE in genes reported to be regulated by other hormones or a biosynthetic precursor of hormone, such as 1-aminocyclopropane-1-carboxylic acid (ACC), indole-3-acetic acid (IAA), methyl jasmonate (MeJA), gibberellins (GA), and cytokinins (CK). Whereas the percentage of genes possessing the BRRE is enriched in the ABA-upregulated group (36.4%) and BR-downregulated group (35.2%) compared to the whole genome control (25%), the percentage was similar for other hormone-response genes (Table 1), except for those upregulated by MeJA, suggesting that BRs negatively regulate JA signaling, as previously noted (Kim et al., 2013).

Of the genes upregulated by ABA and downregulated by BRs, seven encoded ABF transcription factors (Supplementary Table S1). qRT-PCR analysis showed that RD26 and ANAC102 transcription was induced and repressed by ABA and epi-BL, respectively (Fig. 2C). RD26, ANAC102, and ANAC092 encode NAC transcription factors, which contain a NAC domain (Fig. 2D). Moreover, RD26 and ANAC102 are closely clustered in the phylogenetic tree, belonging to the ATAF subfamily of NAC domain proteins (Fujita et al., 2004). We extended our analysis to other genes in the ATAF subfamily, and found that these genes are also regulated by BRs (Fig. 2E). We measured the transcript level of each gene in response to a 3-h treatment with ABA or BRs, and found that all the genes except for ANAC081 were downregulated by BRs (Fig. 2E). Although ANAC081 did not respond to epi-BL, it was reported to be upregulated by NaCl and drought stress (Fujita et al., 2004). Previously, chromatin-immunoprecipitation microarray (ChIP-Chip) experiments revealed that ANAC102, ANAC032, ANAC019, ANAC081, ANAC055, and RD26 are the direct targets of BZR1 (Sun et al., 2010), suggesting that BZR1 directly regulates the expression of these genes. Considering that this subfamily of NACs is regulated by various environmental stimuli in addition to ABA, it is likely that BRs regulate this group of genes to balance growth and stress pathways.

Overexpression of RD26 results in a weak BR-deficient mutant phenotype

Similar to BR mutants, 35Spro:RD26 overexpression lines were previously reported to have round leaf blades and short petioles (Fujita et al., 2004). We thus were given the DNA of 35Spro:RD26 and generated the transgenic lines to re-examine the responses after hormone and stress treatments. We confirmed that RD26 overexpression lines exhibited a semi-dwarf phenotype, with a reduction in leaf size and inflorescence height (Supplementary Fig. S1A). The phenotype was more pronounced in lines with high levels of 35Spro:RD26 expression, suggesting that these phenotypes are attributable to RD26 (Supplementary Figs. S1B and S1C). A contrasting phenotype was observed when RD26 activity was suppressed by an inhibitory SRDX epitope fused to the carboxy-terminus of RD26. Such plants had elongated petioles and downward-curled leaves, which are characteristics of constitutive BR mutants (Chung et al., 2012; Fujita et al., 2004; Kim et al., 2013). These findings suggest that the genetic pathways controlling the stress response and growth are tightly coupled by the actions of BRs and ABA.

Interestingly, previous reports showed that overexpression of other transcription factors involved in the response to abiotic stresses, including ABF3 and ABF4, also resulted in a retarded growth phenotype (Kang et al., 2002). Furthermore, overexpression of the CBF3 transcription factor, which is essential for cold stress tolerance, resulted in a semi-dwarf phenotype (Sakuma et al., 2006). Taken together, it is likely that stress tolerance mechanisms, which protect the plant from abiotic stresses, limit energy-requiring BR-dependent growth.

Transcriptional induction of RD26 in salt stress conditions is inhibited by BRs and stimulated by propiconazole treatment

It was reported that BR mutants are hypersensitive to ABA. Moreover, BR-overproducing and constitutive BR signaling mutants tend to be less tolerant to stresses (Chung et al., 2012; Kim et al., 2013), suggesting that BR negatively regulates stress responses. Since RD26 responds not only to ABA but also to ABA-dependent water stresses (Fujita et al., 2004), we chose RD26 as a marker gene that is antagonistically regulated by BR and ABA during ABA-dependent stresses. To investigate if RD26 transcription is inhibited by BRs when the plant is subjected to stress, we examined RD26 expression in a transgenic Arabidopsis plant expressing RD26pro:GUS. In general, GUS staining was confined to the roots. In mock conditions, the 6-day-old seedlings displayed weak GUS activity in the root region above the elongation zone (Fig. 3A). However, when seedlings were treated with the BR biosynthetic inhibitor propiconazole (Pcz) (Hartwig et al., 2012) for 3 days, GUS expression became markedly stronger. In contrast, GUS expression was barely detectable in the slender roots of seedlings treated with epi-BL (Fig. 3A).

Previously, it was reported that RD26pro:GUS expression was rapidly induced in all tissues by salt stresses (Fujita et al., 2004). When 6-day-old RD26pro:GUS seedlings were incubated in 150 mM NaCl for 2 days, GUS staining was strongly detected, especially in the root tip region (Fig. 3A). To determine the effects of Pcz and BL, seedlings were pre-treated with Pcz or BL for 2 days before being transferred to NaCl media supplemented with Pcz and epi-BL, respectively. Pretreatment with Pcz synergistically induced the expression of RD26pro:GUS in transgenic seedlings subjected to 150 mM NaCl, indicating that Pcz accelerates the induction of RD26 expression in response to stress. However, epi-BL pre-treated samples displayed little staining in the roots, with only marginal induction by NaCl.

To quantify the expression of RD26pro:GUS, root tips (∼5 mm) were excised and GUS activity was measured. Consistently, GUS activity was noticeably increased in samples treated with Pcz, whereas almost no signal was detected in epi-BL-treated samples (Fig. 3B). Moreover, treatment with 200 mM NaCl caused physical damage to plants than treatment with 150 mM NaCl, as tissues disintegrated when the osmotic balance was disrupted. However, the phenotype of roots exposed to 200 mM NaCl alone for 2 days was different from that of samples pre-treated with epi-BL or Pcz and then exposed to 200 mM NaCl for 2 days (Supplementary Fig. S2). The roots of Pcz-treated seedlings were harder and thicker than those treated with epi-BL, which were weak and fragile. Taken together, BRs repress RD26 expression, both in ambient and stress conditions, while Pcz enhances RD26 expression.

BIN2 increases salt stress tolerance

We have demonstrated that BRs repress the expression of the ABA-responsive genes to ameliorate ABA-dependent stress tolerance. To test which component in the BR signaling pathway is the focal point of ABA and BR crosstalk in the salt stress tolerance mechanism, we first examined the salt stress tolerance of wild-type seedlings treated with the BIN2 inhibitors, Lithium (Klein and Melton, 1996; Stambolic et al., 1996) and bikinin (De Rybel et al., 2009). Lithium inhibits BIN2 activity by competing with Mg2+ (Klein and Melton, 1996; Stambolic et al., 1996). In presence of Lithium (LiCl), the effects of NaCl was greatly enhanced such that seedlings turned yellow and died (Fig. 4A). More quantitatively, the survival rate of seedlings treated with 3 mM LiCl was 42% that of control seedlings treated with 3 mM KCl (Figs. 4A and 4B). We obtained the similar results when repeating this experiment using bikinin. Induction of GUS activity in the RD26pro:GUS line by 150 mM NaCl was also inhibited by LiCl and bikinin (Fig. 4D and Supplementary Fig. S3), implying that the low survival rate of plants treated with salt and LiCl was mainly due to the inhibition of ABA-response genes by BRs, especially by the pathway regulated by the BIN2 kinase. Taken together, ABA suppresses the BR pathway, which acts via BIN2, to impart salt stress tolerance.

Conserved motifs in the co-regulated genes

To further understand how the genes are co-regulated by BRs and ABA, we compared the promoter sequences of the gene identified and displayed in Fig. 2. Firstly, we found that the motif sequence conserved among the ABA-upregulated and BR-downregulated genes was clearly an ABRE (motif 1, Fig. 5A). Motif 1 is similar to the BRRE; therefore, it is tempting to suggest that BZR1 and ABF/AREB transcription factors may competitively regulate their target genes by binding to the same response elements.

Secondly, in the case of the BR-up and ABA-downregulated genes, a GAGA motif was enriched (Fig. 5B). Previously, it was reported that BASIC PENTACYSTEINE (BPC) proteins bind to this GAGA motif (Meister et al., 2004; Monfared et al., 2011; Sing et al., 2009). It is likely that BPC may function in the antagonistic regulation of ABA and BR. However, we cannot rule out the possibility that conserved sequences can be bound by currently unidentified transcription factors (Rozhon et al., 2010; Yan et al., 2009).

BR-deficient mutants are known to be hypersensitive to ABA (Steber and McCourt, 2001; Zhang et al., 2009), suggesting that ABA can efficiently induce ABA responses when growth is minimized. Therefore, we identified the genes antagonistically regulated by ABA and BRs, including RD26 and the ANAC genes, which were previously shown to function in various stress responses (Christianson et al., 2010). In addition, we provided evidence that BIN2 is necessary to maintain the balance between ABA and BR signaling under salt stress conditions.

Growth inhibition mechanism under stress conditions

Since it is not fully understood how ABA inhibits growth, we studied the mechanisms controlled by ABA and the growth-promoting BRs. Plants grown in medium supplemented with ABA or NaCl displayed a growth retardation phenotype similar to that of BR-deficient mutants (Fig. 1). One explanation for this is that BR downregulates the genes that may not be directly required for stress-tolerance processes. In support of this, the expression of RD26 and other genes encoding stress-related NAC transcription factors was reduced by treatment with epi-BL. Likewise, elongated-D (elg-D), a gain-of-function allele of BAK1 with an enhanced growth phenotype, exhibited reduced photo-synthetic efficiency upon salt stress, possibly due to the reduced expression of genes involved in stress responses (Chung et al., 2012). Conversely, a recent microarray analysis revealed that many of the cold stress-responsive genes, including WRKY and CBFs, are upregulated in bri1-9, suggesting that BR signaling antagonistically regulates stress-response genes (Kim et al., 2010).

Salt-treated roots tend to break easily and this effect is severe when BR is added. In contrast, when Pcz is added, roots remain thick and relatively intact compared to those subjected to salt treatment alone (Supplementary Fig. S2). In Arabidopsis, cell wall loosening is temporarily required for BR-mediated cell expansion, and this is catalyzed by XYLOGLUCAN ENDOHYDROLASES (XEH) (Fanutti et al., 1993). Previously, it was demonstrated that the salt-responsive transcription factor OsMPS, which downregulates the expression of cell-wall bio-synthetic genes and EXPANSIN (EXP) genes, is repressed by growth hormones such as BRs and auxin, suggesting that OsMPS functions in the crosstalk that balances adaptive growth with survival under salt stress (Schmidt et al., 2013). Pcz treatment might have corrected the altered root shape in plants exposed to salt stress by effective disruption of the BR signaling (Supplementary Fig. S2).

It was interesting to observe that RD26 overexpression resulted in semi-dwarfism similar to that observed in BR mutants (Supplementary Fig. S1). This morphological similarity suggests that RD26 antagonistically regulates the expression of growth-promoting genes regulated by BRs. Indeed, transgenic lines overexpressing RD26 or ABF3 and ABF4 consistently displayed a semi-dwarf phenotype, but enhanced drought tolerance (Kang et al., 2002). Taken together, stress-responsive transcription factors appear to limit energy expenditure on growth to enhance stress tolerance, possibly by downregulating BR-responsive genes.

BR and ABA signaling pathways converge at BIN2

Seedlings in which BIN2 activity was inhibited by either LiCl or bikinin displayed a decreased survival rate when subjected to a salt stress of 200 mM NaCl (Fig. 4). GUS activity was absent in RD26pro:GUS plants treated with LiCl and bikinin. These results suggest that BIN2 controls the expression of genes involved in salt stress tolerance, including RD26. BIN2 is a protein kinase that phosphorylates BR-specific transcription factors, such as BZR1 and BES1. It is possible that BIN2 regulates stress-associated genes, especially those that are upregulated by ABA and downregulated by BR, through controlling the activities of BZR1 and BES1. Additionally, overexpression of AtGSK1, the closest homolog of BIN2, results in enhanced salt stress tolerance in Arabidopsis, suggesting that BIN2 may function in the salt stress response (Piao et al., 2001). Based on these findings, we propose a model that illustrates the interaction between BRs and ABA in controlling growth and stress tolerance (Supplementary Fig. S4).

We predict that salt stress controls a step below BIN2 in the BR signaling pathway, because NaCl treatment in combination with BIN2 inhibition altered the expression of RD26 and rendered the seedlings less tolerant than those treated with salt alone. Future research should examine how NaCl signals modify the activity of BIN2. The underlying mechanism may function directly or indirectly through another signaling component that has yet to be discovered.

In conclusion, we sought to determine why stressed plants display stunted growth. We analyzed the relationship between BRs, which promote growth, and ABA, which is involved in the response to environmental stress. Based on the phenotypic similarities between ABA-treated seedlings and bri1-9, we searched for and identified genes that are oppositely regulated by ABA and BRs in previously reported microarray data sets. Of these genes, RD26, which belongs to the ANAC family, was chosen as representative and shown to be specifically induced by ABA, but suppressed by BRs. We provided evidence that BIN2 plays a key role in balancing the growth and the stress responses during periods of stress. Thus, our results suggest that ABA and BRs may regulate a set of target genes to fine-tune Arabidopsis growth during the stress response.

Fig. 1. Response of wild-type and bri1-9 seedlings to ABA treatment. (A) Top view of Arabidopsis wild-type seedlings treated with mock or ABA, and bri1-9 treated with mock only. Scale bar = 0.5 cm. (B) Whole seedling morphology of 10-day-old Col and bri1-9 plants. From left, mock-treated wild type, ABA-treated wild type, and bri1-9. Scale bar = 1 cm. (C) Statistical representation of the dose-dependent effect of ABA on root growth. Seedlings were germinated on MS medium before being transferred to medium containing 0, 2, 4, or 8 μM ABA for a further 5 days of growth. The growth of bri1-9 roots was retarded to a greater extent by ABA treatment than was that of wild-type roots. Values show root length relative to that of an untreated wild-type control. (D) Germination of Col and bri1-9 on ABA-supplemented media. Photographs were taken ten days after sowing. Germination is suppressed to a greater extent in the bri1-9 plates. (E) Statistical analysis of germination rates in response to different ABA doses. Seeds with visible radicles were scored as successful germination events. Average values are represented with standard deviations of three independent biological replicates. Again, bri1-9 was more sensitive than the wild type to ABA treatment. (F) Establishment of green cotyledons in the presence of ABA. Seedlings with green cotyledons were scored. Error bars in (C, E, and F) are standard deviations (n = 3).
Fig. 2. Identification of genes co-regulated by BRs and ABA in publicly available microarray data. (A) Venn diagram of ABA- and BR-responsive genes. Genes that are antagonistically regulated by these hormones were selected from previously-reported data sets (). Left, Venn diagram of genes downregulated by BRs but upregulated by ABA; right, genes upregulated by BRs but downregulated by ABA. Fisher’s exact test was conducted to determine the p-value of overlapping genes (P < 0.09 for genes upregulated by ABA and downregulated by BR; P < 0.0051 for genes downregulated by ABA and upregulated by BR). (B) Enrichment of the BR-response element (BRRE) in the -1000 bp promoter sequences of 62 and 50 genes co-regulated by BRs and ABA, respectively. The percentage of genes that harbor at least one BRRE (CGTG[T/C][G/A]) was determined by searching the Arabidopsis genome sequence database. (C) Time-course analysis of RD26 and ANAC102 transcript levels in seven-day-old wild-type seedlings treated with 1 μM epi-BL or 50 μM ABA in liquid MS media. Results were normalized using UBQ10, and converted to values relative to a mock-treated control. Data are mean ± standard deviation of three technical replicates. (D) RD26 belongs to the NAC transcription factor family, which is composed of at least 94 members (). Of the entire phylogenetic tree of this gene family, a clade containing RD26 is shown. The length of the bar indicates the number of changes in amino acid residues per unit length of the horizontal branches. (E) qRT-PCR analysis of the expression of ANAC genes clustered with RD26 in (D). UBQ10 levels were used as loading controls. Besides ANAC081, all tested ANAC genes responded similarly to RD26; i.e., they were upregulated in response to ABA, and downregulated after exposure to epi-BL.
Fig. 3. BR-mediated regulation of RD26. (A) GUS histochemical staining pattern of RD26pro:GUS seedlings. Four-day-old RD26pro:GUS seedlings were transferred to media containing epi-BL or Pcz and further incubated for two days (left panel), or transferred to media containing 150 mM NaCl plus the indicated chemicals and incubated for two more days. Scale bar = 0.5 mm. (B) Quantitative assay of GUS activity using the bottom 5 mm of tissue from root tips. Error bars represent ± SE (N > 12).
Fig. 4. Reduction in salt stress tolerance upon inhibition of BIN2. (A) Morphology of seedlings treated with mock or various salts. Seedlings were treated separately and arranged in a new plate to obtain a collective image of responses. First row, mock-treated control. Second row, treatment with KCl or LiCl alone. Third row, NaCl treatment in combination with KCl or LiCl. Scale bar = 5 mm. (B, C) Survival rate of Arabidopsis seedlings grown in 150 mM (B) or 200 mM NaCl media (C) supplemented with salts or bikinin (a BIN2 inhibitor). Survival rate was measured as the ratio of the number of green vs. pale yellow seedlings. Error bar = SD (n = 3). (D) GUS staining pattern in the roots of RD26pro:GUS seedlings. Scale bar = 1 mm.
Fig. 5. Consensus sequence elements in the promoter of genes co-regulated by both ABA and BRs. The top fourmost over-represented motifs found in the -1000 bp proximal promoter of genes are shown. Genes that are (A) upregulated by ABA and downregulated by BR and (B) downregulated by ABA and upregulated by BR. Sequence logos for (A) and (B) were generated using the MEME analysis tool. The total information content of each logo is given in bits; the height of each nucleotide in the logo represents the positional probability of that nucleotide multiplied by the information content of the logo. E-value means the possibility of finding the motifs merely by chance.
Table 1.

. Proportion of genes containing the BRRE

ABABRsACCIAAGAMeJaCK
Up or DownUDUDUDUDUDUDUD
No. genes144014762683831673654303554082806701332163
BRRE-containing gene5243565913545871237811262721818146
BRRE/Total36.424.122.035.226.923.828.622.027.531.733.725.824.428.2

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Article

Research Article

Mol. Cells 2014; 37(11): 795-803

Published online November 30, 2014 https://doi.org/10.14348/molcells.2014.0127

Copyright © The Korean Society for Molecular and Cellular Biology.

Antagonistic Regulation of Arabidopsis Growth by Brassinosteroids and Abiotic Stresses

Yuhee Chung1,4, Soon Il Kwon2, and Sunghwa Choe1,2,3,*

1School of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea, 2Convergence Research Center for Functional Plant Products, Advanced Institutes of Convergence Technology, Suwon 443-270, Korea, 3Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea, 4Present address: Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, USA

Correspondence to:*Correspondence: shchoe@snu.ac.kr

Received: May 15, 2014; Revised: September 6, 2014; Accepted: September 11, 2014

Abstract

To withstand ever-changing environmental stresses, plants are equipped with phytohormone-mediated stress resistance mechanisms. Salt stress triggers abscisic acid (ABA) signaling, which enhances stress tolerance at the expense of growth. ABA is thought to inhibit the action of growth-promoting hormones, including brassinosteroids (BRs). However, the regulatory mechanisms that coordinate ABA and BR activity remain to be discovered. We noticed that ABA-treated seedlings exhibited small, round leaves and short roots, a phenotype that is characteristic of the BR signaling mutant, brassinosteroid insensitive1-9 (bri1-9). To identify genes that are antagonistically regulated by ABA and BRs, we examined published Arabidopsis microarray data sets. Of the list of genes identified, those upregulated by ABA but downregulated by BRs were enriched with a BRRE motif in their promoter sequences. After validating the microarray data using quantitative RT-PCR, we focused on RD26, which is induced by salt stress. Histochemical analysis of transgenic Arabidopsis plants expressing RD26pro:GUS revealed that the induction of GUS expression after NaCl treatment was suppressed by co-treatment with BRs, but enhanced by co-treatment with propiconazole, a BR biosynthetic inhibitor. Similarly, treatment with bikinin, an inhibitor of BIN2 kinase, not only inhibited RD26 expression, but also reduced the survival rate of the plant following exposure to salt stress. Our results suggest that ABA and BRs act antagonistically on their target genes at or after the BIN2 step in BR signaling pathways, and suggest a mechanism by which plants fine-tune their growth, particularly when stress responses and growth compete for resources.

Keywords: ABA, abiotic stress, BIN2, brassinosteroids, RD26, Root

INTRODUCTION

Due to their sessile nature, plants have developed strategies to cope with abiotic challenges and biotic stresses (Chung et al., 2012; Kim et al., 2014; Maharjan and Choe, 2011). Plants exposed to abiotic stresses display severe growth retardation and reduced productivity. Growth is regulated by plant hormones, which modify endogenous programs in response to exogenous signals. However, the hormone-dependent mechanisms by which growth is inhibited under stress conditions are not fully understood. The molecular mechanisms that impart tolerance to water stress can be divided into abscisic acid (ABA)-dependent and ABA-independent pathways (Shinozaki and Yamaguchi-Shinozaki, 2007). ABA plays vital roles in adaptation to environmental changes, seed dormancy, and the regulation of stomatal closure (Grill and Himmelbach, 1998; Lee and Luan, 2012).

Under stressed conditions, plants rapidly produce ABA, which stimulates the resistance mechanism. In the ABA-dependent pathway, ABA binds to soluble receptors of the PYRABACTIN RESISTANCE1 (PYR1)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS (RCARs) family, which induces the de novo synthesis of ABA through 9-cis epoxycarotenoid dioxygenase (NCED) as part of a positive feedback mechanism (Ma et al., 2009; Park et al., 2009). Once ABA activates SnRK2s, SnRK2s phosphorylate and thereby activate the transcription of ABA-dependent transcription factors, such as ABA-responsive element binding factors (ABFs/AREBs) (Furihata et al., 2006; Uno et al., 2000). ABFs/AREBs then bind to the ABA response element (ABRE) in the promoter region of their target genes (Mundy et al., 1990). These conserved elements contain PyACGTGGC (Busk and Pages, 1997; Guiltinan et al., 1990; Yamaguchi-Shinozaki et al., 1990) and ACGTG[G/T]C (Hobo et al., 1999) residues. ABA regulates approximately 10% of the genes in Arabidopsis, and many of these genes are also regulated by other hormones (Nemhauser et al., 2006).

In addition to ABFs/AREBs, other ABA-induced transcription factors are known to participate in the ABA response and stress tolerance. For instance, the NAC (NAM, ATAF1/2 and CUC2) transcription factor family, which largely consists of NO APICAL MERISTEM (NAM) and Arabidopsis thaliana transcription activation factor (ATAF1/2) transcription factors, is known to function in the stress response (Aida et al., 1997). ATAF1/ANAC002 directly regulates ABA biosynthesis through the transcriptional activation of NCED3 (Jensen et al., 2013; Tran et al., 2004). RD26 is a member of the ATAF family and is reported to function in ABA-dependent stress-response pathways (Fujita et al., 2004; Ooka et al., 2003).

Brassinosteroids (BRs) are a class of plant steroidal hormones (Chung and Choe, 2013). Like mammalian steroid hormones such as estrogen, ecdysone, and progesterone, BRs play key roles in plant development, regulating processes such as cell elongation, vascular system differentiation, senescence, and stress responses (Choe, 2006; Clouse and Sasse, 1998). BRs and other phytohormones have numerous target genes in common, and complex crosstalk mechanisms exist among these hormone signal transduction pathways (Chung et al., 2011; Nemhauser et al., 2006). Brassinolide (BL), the most active form of BRs, binds to an island domain in the extracellular domain of BRASSINOSTEROID INSENSITIVE 1 (BRI1) (Kinoshita et al., 2005; Sun et al., 2013). In the absence of BL, BKI1 binds to the cytoplasmic kinase domain of BRI1 and thereby inhibits its phosphorylation function (Wang et al., 2008). However, when BL binds to BRI1, BKI1 is released from BRI1 and BRI1 forms a heterodimer with BRI1-ASSOCIATED-KINASE 1 (BAK1) (Russinova et al., 2004; Wang and Chory, 2006). Then, BR-SIGNALING KINASE 1 (BSK1) is released from the cytoplasmic domain of BRI1 and transduces the signal into the nucleus via a protein phosphatase, bri1 SUPPRESSOR1 (BSU1) (Kim et al., 2009; Tang et al., 2008). BSU1 inactivates the BR-INSENSITIVE 2 (BIN2) kinase that acts as a negative regulator in BR signaling pathways (Choe et al., 2002; Li and Nam, 2002; Li et al., 2001). BIN2 negatively regulates BR-specific transcription factors, including BZR1 and BES1 by phosphorylation (Kim et al., 2009), and is degraded in response to BL (Peng et al., 2008). BZR1 binds to the BR response element (BRRE) motif (CGTG[T/C][G/A]) (He et al., 2005) to both activate BR response genes and inhibit BR biosynthetic genes, including DWF4 (Choe et al., 2001; Kim et al., 2006; 2013). Weak alleles of bri1 include bri1-5 (Noguchi et al., 1999) and bri1-9, and exhibits a semi-dwarf phenotype (Jin et al., 2007).

In contrast to the ABA pathway, the majority of signaling components have been elucidated in the BR signaling cascade (Vriet et al., 2013). Given the importance of ABA and BRs, much research has focused on identifying the mechanism of crosstalk between BRs and ABA. It has been demonstrated that ABA and BRs antagonistically regulate each other during seed germination and root growth inhibition (Steber and McCourt, 2001; Zhang et al., 2009)

In this study, we sought to understand the mechanisms by which BRs and ABA interact. First, we selected putative marker genes that are antagonistically regulated by BRs and ABA from a microarray database deposited in AtGenExpress (Nemhauser et al., 2006). Secondly, we found that chemical inhibition of BIN2 decreased the plant’s tolerance to salt stress, suggesting that BIN2 is involved in ABA-mediated salt tolerance processes. Based on our findings, we propose a model in which transcription factors that bind to common target genes and are specific to either BRs or ABA are antagonistically regulated by each other to bring about ABA-dependent stress responses.

MATERIALS AND METHODS

Plant material and growth conditions

Arabidopsis plants of Columbia ecotype were grown in 0.5×Murashige and Skoog (MS) medium containing 0.5% sucrose and 0.8% plant agar. Plants or seedlings were kept in a growth room at 22°C with a 16 h light/8 h dark cycle. To measure the survival rate in salt media, seeds were germinated and grown in MS agar medium and transferred to medium containing the indicated concentrations of hormone or chemical. After 1 day, seedlings were transferred again to medium containing NaCl. epi-Brassinolide (BL) was dissolved in DMSO, and ABA stock was prepared in ethyl alcohol (EtOH). The controls contained the same volume of DMSO or EtOH as chemicals added to the treated aliquots, and considered a mock treatment.

Quantitative RT-PCR

RNA extraction and cDNA synthesis were conducted according to a previous report (Chung et al., 2012). Quantitative RT-PCR analysis was performed using SYBR-mix (KAPA Biosystems). UBQ10 was used as an internal control. Primer sets used for PCR are listed in Supplementary Table S2.

GUS histochemical assay and quantification of GUS activity

Five-day-old RD26pro:GUS transgenic seedlings were first treated with the indicated concentrations of hormone or chemical. Following pre-incubation, each seedling was transferred to NaCl-containing agar medium supplemented with the same concentration of hormone or chemical. After 3 days, seedlings were transferred to GUS buffer (1 mM 5-bromo-4-chloro-3-indoyl-β-d-GlcUA, 100 mM sodium phosphate (pH 7), 5 mM potassium ferrocyanide, 5 mM potassium ferricyanide, 10 mM EDTA, and 0.1% (v/v) Triton X-100) and incubated for 2 h. Serially-diluted EtOH was used to clear the chloroplasts and to reduce background staining. Micrographs were taken using a stereomicroscope (Olympus). To quantify the in vivo GUS activity of RD26pro:GUS in each treatment, 0.5 cm of the root tip of treated seedlings was excised and transferred to 96-well plates pre-filled with a substrate solution (Blazquez et al., 1998). Seedlings in the substrate solution were incubated for 1 h at 37°C and the reaction was stopped by the addition of 100 μl of cold 0.2 M Na2CO3 solution. The fluorescence intensity was measured using a fluorescence spectrophotometer (Varian, USA) with an excitation wavelength of 360 nm and an emission wavelength of 465 nm. The values of 12 seedlings were averaged and plotted with their standard error. The standard curve was calculated using known concentrations of 4-methylumbelliferol solution.

Motif prediction by MEME

MEME (http://meme.sdsc.edu) was used to search for motifs conserved in the promoter region 1000 bp upstream of the start codons of genes antagonistically regulated by ABA and BR (Bailey and Elkan, 1995). A MEME search revealed that the optimum width for motifs was 6 to 9 bp.

RESULTS

Morphological similarity between ABA-treated seedlings and the BR-deficient dwarf mutant

We observed that treatment of Arabidopsis seedlings with ABA often resulted in phenotypes that resembled those of BR-deficient dwarf mutants. The small, curled leaves of ABA-treated Col wild-type plants were similar to those of mock-treated bri1-9 plants (Figs. 1A and 1B), which bear a loss-of-function mutation in the BR receptor (Jin et al., 2007). Previously, we also showed that BR mutants are more sensitive to ABA treatment (Choe et al., 2002). These findings suggest that ABA and BRs interact to regulate Arabidopsis growth.

Because ABA treatment mimicked the BR mutant phenotype, we reasoned that bri1-9 would be more sensitive to ABA than the wild type. To test this, we performed a dose-response assay in which we examined the key characteristics of seedling development, including root growth, germination, and post-germination growth, under various concentrations of ABA. The root growth rate of wild-type plants was reduced in response to ABA treatment in a dose-dependent manner, and the degree of reduction was much greater in bri1-9 (Fig. 1C). In addition, we scored the percentage of seeds with emerged radicles 3 days after sowing on mock, 0.4, 0.8, and 1.2 μM ABA medium (Fig. 1D). On 0.8 μM ABA, 80% of the Col seeds germinated, whereas only 25% of bri1-9 seeds did, suggesting that bri1-9 is more sensitive to exogenous ABA treatment than is the wild type (Fig. 1E). Of the germinated seeds, only 55% and 19% of the cotyledons of wild-type and bri1-9 seedlings remained green, respectively, at 0.8 μM ABA (Fig. 1F). Thus, the growth of bri1-9 plants was more sensitive to ABA than the wild type, suggesting that ABA controls BR signaling pathways to achieve optimal growth and development during the ABA-mediated stress response.

BRs and ABA antagonistically regulate overlapping sets of genes

To identify the genes that are oppositely regulated by ABA and BRs, we analyzed a set of publicly available microarray data that were reported by Nemhauser et al. (2006). They reported that 383 genes upregulated by BRs, 268 were downregulated by BRs, 1440 were upregulated by ABA, and 1476 were downregulated by ABA (Nemhauser et al., 2006). Because BRs and ABA have a tendency to reverse the effects on Arabidopsis growth (Fig. 1), we focused on genes that respond oppositely to BRs and ABA. We determined the union (62) of genes downregulated by BRs and upregulated by ABA, and the union (50) upregulated by BRs and downregulated by ABA (Fig. 2A). These genes were chosen for further investigation.

Because BZR1 can function either as an inducer or repressor of BR-responsive genes (He et al., 2005), we determined the number of BR-response elements (BRREs, CGTG[TC][GA], (He et al., 2005)) in the promoter DNA sequences of these genes (Fig. 2B). Whereas 25% of genes in the whole genome contained the BRRE motif, 48% of genes upregulated by ABA and downregulated by BR contained this motif (Fig. 2B). Since the BRRE was not enriched in the group of genes downregulated by ABA and upregulated by BR, we propose that genes that are upregulated by ABA and downregulated by BR are likely targeted by BZR1 through direct binding to BRRE in the promoter sequences.

We next determined the frequency of the BRRE in genes reported to be regulated by other hormones or a biosynthetic precursor of hormone, such as 1-aminocyclopropane-1-carboxylic acid (ACC), indole-3-acetic acid (IAA), methyl jasmonate (MeJA), gibberellins (GA), and cytokinins (CK). Whereas the percentage of genes possessing the BRRE is enriched in the ABA-upregulated group (36.4%) and BR-downregulated group (35.2%) compared to the whole genome control (25%), the percentage was similar for other hormone-response genes (Table 1), except for those upregulated by MeJA, suggesting that BRs negatively regulate JA signaling, as previously noted (Kim et al., 2013).

Of the genes upregulated by ABA and downregulated by BRs, seven encoded ABF transcription factors (Supplementary Table S1). qRT-PCR analysis showed that RD26 and ANAC102 transcription was induced and repressed by ABA and epi-BL, respectively (Fig. 2C). RD26, ANAC102, and ANAC092 encode NAC transcription factors, which contain a NAC domain (Fig. 2D). Moreover, RD26 and ANAC102 are closely clustered in the phylogenetic tree, belonging to the ATAF subfamily of NAC domain proteins (Fujita et al., 2004). We extended our analysis to other genes in the ATAF subfamily, and found that these genes are also regulated by BRs (Fig. 2E). We measured the transcript level of each gene in response to a 3-h treatment with ABA or BRs, and found that all the genes except for ANAC081 were downregulated by BRs (Fig. 2E). Although ANAC081 did not respond to epi-BL, it was reported to be upregulated by NaCl and drought stress (Fujita et al., 2004). Previously, chromatin-immunoprecipitation microarray (ChIP-Chip) experiments revealed that ANAC102, ANAC032, ANAC019, ANAC081, ANAC055, and RD26 are the direct targets of BZR1 (Sun et al., 2010), suggesting that BZR1 directly regulates the expression of these genes. Considering that this subfamily of NACs is regulated by various environmental stimuli in addition to ABA, it is likely that BRs regulate this group of genes to balance growth and stress pathways.

Overexpression of RD26 results in a weak BR-deficient mutant phenotype

Similar to BR mutants, 35Spro:RD26 overexpression lines were previously reported to have round leaf blades and short petioles (Fujita et al., 2004). We thus were given the DNA of 35Spro:RD26 and generated the transgenic lines to re-examine the responses after hormone and stress treatments. We confirmed that RD26 overexpression lines exhibited a semi-dwarf phenotype, with a reduction in leaf size and inflorescence height (Supplementary Fig. S1A). The phenotype was more pronounced in lines with high levels of 35Spro:RD26 expression, suggesting that these phenotypes are attributable to RD26 (Supplementary Figs. S1B and S1C). A contrasting phenotype was observed when RD26 activity was suppressed by an inhibitory SRDX epitope fused to the carboxy-terminus of RD26. Such plants had elongated petioles and downward-curled leaves, which are characteristics of constitutive BR mutants (Chung et al., 2012; Fujita et al., 2004; Kim et al., 2013). These findings suggest that the genetic pathways controlling the stress response and growth are tightly coupled by the actions of BRs and ABA.

Interestingly, previous reports showed that overexpression of other transcription factors involved in the response to abiotic stresses, including ABF3 and ABF4, also resulted in a retarded growth phenotype (Kang et al., 2002). Furthermore, overexpression of the CBF3 transcription factor, which is essential for cold stress tolerance, resulted in a semi-dwarf phenotype (Sakuma et al., 2006). Taken together, it is likely that stress tolerance mechanisms, which protect the plant from abiotic stresses, limit energy-requiring BR-dependent growth.

Transcriptional induction of RD26 in salt stress conditions is inhibited by BRs and stimulated by propiconazole treatment

It was reported that BR mutants are hypersensitive to ABA. Moreover, BR-overproducing and constitutive BR signaling mutants tend to be less tolerant to stresses (Chung et al., 2012; Kim et al., 2013), suggesting that BR negatively regulates stress responses. Since RD26 responds not only to ABA but also to ABA-dependent water stresses (Fujita et al., 2004), we chose RD26 as a marker gene that is antagonistically regulated by BR and ABA during ABA-dependent stresses. To investigate if RD26 transcription is inhibited by BRs when the plant is subjected to stress, we examined RD26 expression in a transgenic Arabidopsis plant expressing RD26pro:GUS. In general, GUS staining was confined to the roots. In mock conditions, the 6-day-old seedlings displayed weak GUS activity in the root region above the elongation zone (Fig. 3A). However, when seedlings were treated with the BR biosynthetic inhibitor propiconazole (Pcz) (Hartwig et al., 2012) for 3 days, GUS expression became markedly stronger. In contrast, GUS expression was barely detectable in the slender roots of seedlings treated with epi-BL (Fig. 3A).

Previously, it was reported that RD26pro:GUS expression was rapidly induced in all tissues by salt stresses (Fujita et al., 2004). When 6-day-old RD26pro:GUS seedlings were incubated in 150 mM NaCl for 2 days, GUS staining was strongly detected, especially in the root tip region (Fig. 3A). To determine the effects of Pcz and BL, seedlings were pre-treated with Pcz or BL for 2 days before being transferred to NaCl media supplemented with Pcz and epi-BL, respectively. Pretreatment with Pcz synergistically induced the expression of RD26pro:GUS in transgenic seedlings subjected to 150 mM NaCl, indicating that Pcz accelerates the induction of RD26 expression in response to stress. However, epi-BL pre-treated samples displayed little staining in the roots, with only marginal induction by NaCl.

To quantify the expression of RD26pro:GUS, root tips (∼5 mm) were excised and GUS activity was measured. Consistently, GUS activity was noticeably increased in samples treated with Pcz, whereas almost no signal was detected in epi-BL-treated samples (Fig. 3B). Moreover, treatment with 200 mM NaCl caused physical damage to plants than treatment with 150 mM NaCl, as tissues disintegrated when the osmotic balance was disrupted. However, the phenotype of roots exposed to 200 mM NaCl alone for 2 days was different from that of samples pre-treated with epi-BL or Pcz and then exposed to 200 mM NaCl for 2 days (Supplementary Fig. S2). The roots of Pcz-treated seedlings were harder and thicker than those treated with epi-BL, which were weak and fragile. Taken together, BRs repress RD26 expression, both in ambient and stress conditions, while Pcz enhances RD26 expression.

BIN2 increases salt stress tolerance

We have demonstrated that BRs repress the expression of the ABA-responsive genes to ameliorate ABA-dependent stress tolerance. To test which component in the BR signaling pathway is the focal point of ABA and BR crosstalk in the salt stress tolerance mechanism, we first examined the salt stress tolerance of wild-type seedlings treated with the BIN2 inhibitors, Lithium (Klein and Melton, 1996; Stambolic et al., 1996) and bikinin (De Rybel et al., 2009). Lithium inhibits BIN2 activity by competing with Mg2+ (Klein and Melton, 1996; Stambolic et al., 1996). In presence of Lithium (LiCl), the effects of NaCl was greatly enhanced such that seedlings turned yellow and died (Fig. 4A). More quantitatively, the survival rate of seedlings treated with 3 mM LiCl was 42% that of control seedlings treated with 3 mM KCl (Figs. 4A and 4B). We obtained the similar results when repeating this experiment using bikinin. Induction of GUS activity in the RD26pro:GUS line by 150 mM NaCl was also inhibited by LiCl and bikinin (Fig. 4D and Supplementary Fig. S3), implying that the low survival rate of plants treated with salt and LiCl was mainly due to the inhibition of ABA-response genes by BRs, especially by the pathway regulated by the BIN2 kinase. Taken together, ABA suppresses the BR pathway, which acts via BIN2, to impart salt stress tolerance.

Conserved motifs in the co-regulated genes

To further understand how the genes are co-regulated by BRs and ABA, we compared the promoter sequences of the gene identified and displayed in Fig. 2. Firstly, we found that the motif sequence conserved among the ABA-upregulated and BR-downregulated genes was clearly an ABRE (motif 1, Fig. 5A). Motif 1 is similar to the BRRE; therefore, it is tempting to suggest that BZR1 and ABF/AREB transcription factors may competitively regulate their target genes by binding to the same response elements.

Secondly, in the case of the BR-up and ABA-downregulated genes, a GAGA motif was enriched (Fig. 5B). Previously, it was reported that BASIC PENTACYSTEINE (BPC) proteins bind to this GAGA motif (Meister et al., 2004; Monfared et al., 2011; Sing et al., 2009). It is likely that BPC may function in the antagonistic regulation of ABA and BR. However, we cannot rule out the possibility that conserved sequences can be bound by currently unidentified transcription factors (Rozhon et al., 2010; Yan et al., 2009).

DISCUSSION

BR-deficient mutants are known to be hypersensitive to ABA (Steber and McCourt, 2001; Zhang et al., 2009), suggesting that ABA can efficiently induce ABA responses when growth is minimized. Therefore, we identified the genes antagonistically regulated by ABA and BRs, including RD26 and the ANAC genes, which were previously shown to function in various stress responses (Christianson et al., 2010). In addition, we provided evidence that BIN2 is necessary to maintain the balance between ABA and BR signaling under salt stress conditions.

Growth inhibition mechanism under stress conditions

Since it is not fully understood how ABA inhibits growth, we studied the mechanisms controlled by ABA and the growth-promoting BRs. Plants grown in medium supplemented with ABA or NaCl displayed a growth retardation phenotype similar to that of BR-deficient mutants (Fig. 1). One explanation for this is that BR downregulates the genes that may not be directly required for stress-tolerance processes. In support of this, the expression of RD26 and other genes encoding stress-related NAC transcription factors was reduced by treatment with epi-BL. Likewise, elongated-D (elg-D), a gain-of-function allele of BAK1 with an enhanced growth phenotype, exhibited reduced photo-synthetic efficiency upon salt stress, possibly due to the reduced expression of genes involved in stress responses (Chung et al., 2012). Conversely, a recent microarray analysis revealed that many of the cold stress-responsive genes, including WRKY and CBFs, are upregulated in bri1-9, suggesting that BR signaling antagonistically regulates stress-response genes (Kim et al., 2010).

Salt-treated roots tend to break easily and this effect is severe when BR is added. In contrast, when Pcz is added, roots remain thick and relatively intact compared to those subjected to salt treatment alone (Supplementary Fig. S2). In Arabidopsis, cell wall loosening is temporarily required for BR-mediated cell expansion, and this is catalyzed by XYLOGLUCAN ENDOHYDROLASES (XEH) (Fanutti et al., 1993). Previously, it was demonstrated that the salt-responsive transcription factor OsMPS, which downregulates the expression of cell-wall bio-synthetic genes and EXPANSIN (EXP) genes, is repressed by growth hormones such as BRs and auxin, suggesting that OsMPS functions in the crosstalk that balances adaptive growth with survival under salt stress (Schmidt et al., 2013). Pcz treatment might have corrected the altered root shape in plants exposed to salt stress by effective disruption of the BR signaling (Supplementary Fig. S2).

It was interesting to observe that RD26 overexpression resulted in semi-dwarfism similar to that observed in BR mutants (Supplementary Fig. S1). This morphological similarity suggests that RD26 antagonistically regulates the expression of growth-promoting genes regulated by BRs. Indeed, transgenic lines overexpressing RD26 or ABF3 and ABF4 consistently displayed a semi-dwarf phenotype, but enhanced drought tolerance (Kang et al., 2002). Taken together, stress-responsive transcription factors appear to limit energy expenditure on growth to enhance stress tolerance, possibly by downregulating BR-responsive genes.

BR and ABA signaling pathways converge at BIN2

Seedlings in which BIN2 activity was inhibited by either LiCl or bikinin displayed a decreased survival rate when subjected to a salt stress of 200 mM NaCl (Fig. 4). GUS activity was absent in RD26pro:GUS plants treated with LiCl and bikinin. These results suggest that BIN2 controls the expression of genes involved in salt stress tolerance, including RD26. BIN2 is a protein kinase that phosphorylates BR-specific transcription factors, such as BZR1 and BES1. It is possible that BIN2 regulates stress-associated genes, especially those that are upregulated by ABA and downregulated by BR, through controlling the activities of BZR1 and BES1. Additionally, overexpression of AtGSK1, the closest homolog of BIN2, results in enhanced salt stress tolerance in Arabidopsis, suggesting that BIN2 may function in the salt stress response (Piao et al., 2001). Based on these findings, we propose a model that illustrates the interaction between BRs and ABA in controlling growth and stress tolerance (Supplementary Fig. S4).

We predict that salt stress controls a step below BIN2 in the BR signaling pathway, because NaCl treatment in combination with BIN2 inhibition altered the expression of RD26 and rendered the seedlings less tolerant than those treated with salt alone. Future research should examine how NaCl signals modify the activity of BIN2. The underlying mechanism may function directly or indirectly through another signaling component that has yet to be discovered.

In conclusion, we sought to determine why stressed plants display stunted growth. We analyzed the relationship between BRs, which promote growth, and ABA, which is involved in the response to environmental stress. Based on the phenotypic similarities between ABA-treated seedlings and bri1-9, we searched for and identified genes that are oppositely regulated by ABA and BRs in previously reported microarray data sets. Of these genes, RD26, which belongs to the ANAC family, was chosen as representative and shown to be specifically induced by ABA, but suppressed by BRs. We provided evidence that BIN2 plays a key role in balancing the growth and the stress responses during periods of stress. Thus, our results suggest that ABA and BRs may regulate a set of target genes to fine-tune Arabidopsis growth during the stress response.

Supplementary information

Fig 1.

Figure 1.Response of wild-type and bri1-9 seedlings to ABA treatment. (A) Top view of Arabidopsis wild-type seedlings treated with mock or ABA, and bri1-9 treated with mock only. Scale bar = 0.5 cm. (B) Whole seedling morphology of 10-day-old Col and bri1-9 plants. From left, mock-treated wild type, ABA-treated wild type, and bri1-9. Scale bar = 1 cm. (C) Statistical representation of the dose-dependent effect of ABA on root growth. Seedlings were germinated on MS medium before being transferred to medium containing 0, 2, 4, or 8 μM ABA for a further 5 days of growth. The growth of bri1-9 roots was retarded to a greater extent by ABA treatment than was that of wild-type roots. Values show root length relative to that of an untreated wild-type control. (D) Germination of Col and bri1-9 on ABA-supplemented media. Photographs were taken ten days after sowing. Germination is suppressed to a greater extent in the bri1-9 plates. (E) Statistical analysis of germination rates in response to different ABA doses. Seeds with visible radicles were scored as successful germination events. Average values are represented with standard deviations of three independent biological replicates. Again, bri1-9 was more sensitive than the wild type to ABA treatment. (F) Establishment of green cotyledons in the presence of ABA. Seedlings with green cotyledons were scored. Error bars in (C, E, and F) are standard deviations (n = 3).
Molecules and Cells 2014; 37: 795-803https://doi.org/10.14348/molcells.2014.0127

Fig 2.

Figure 2.Identification of genes co-regulated by BRs and ABA in publicly available microarray data. (A) Venn diagram of ABA- and BR-responsive genes. Genes that are antagonistically regulated by these hormones were selected from previously-reported data sets (). Left, Venn diagram of genes downregulated by BRs but upregulated by ABA; right, genes upregulated by BRs but downregulated by ABA. Fisher’s exact test was conducted to determine the p-value of overlapping genes (P < 0.09 for genes upregulated by ABA and downregulated by BR; P < 0.0051 for genes downregulated by ABA and upregulated by BR). (B) Enrichment of the BR-response element (BRRE) in the -1000 bp promoter sequences of 62 and 50 genes co-regulated by BRs and ABA, respectively. The percentage of genes that harbor at least one BRRE (CGTG[T/C][G/A]) was determined by searching the Arabidopsis genome sequence database. (C) Time-course analysis of RD26 and ANAC102 transcript levels in seven-day-old wild-type seedlings treated with 1 μM epi-BL or 50 μM ABA in liquid MS media. Results were normalized using UBQ10, and converted to values relative to a mock-treated control. Data are mean ± standard deviation of three technical replicates. (D) RD26 belongs to the NAC transcription factor family, which is composed of at least 94 members (). Of the entire phylogenetic tree of this gene family, a clade containing RD26 is shown. The length of the bar indicates the number of changes in amino acid residues per unit length of the horizontal branches. (E) qRT-PCR analysis of the expression of ANAC genes clustered with RD26 in (D). UBQ10 levels were used as loading controls. Besides ANAC081, all tested ANAC genes responded similarly to RD26; i.e., they were upregulated in response to ABA, and downregulated after exposure to epi-BL.
Molecules and Cells 2014; 37: 795-803https://doi.org/10.14348/molcells.2014.0127

Fig 3.

Figure 3.BR-mediated regulation of RD26. (A) GUS histochemical staining pattern of RD26pro:GUS seedlings. Four-day-old RD26pro:GUS seedlings were transferred to media containing epi-BL or Pcz and further incubated for two days (left panel), or transferred to media containing 150 mM NaCl plus the indicated chemicals and incubated for two more days. Scale bar = 0.5 mm. (B) Quantitative assay of GUS activity using the bottom 5 mm of tissue from root tips. Error bars represent ± SE (N > 12).
Molecules and Cells 2014; 37: 795-803https://doi.org/10.14348/molcells.2014.0127

Fig 4.

Figure 4.Reduction in salt stress tolerance upon inhibition of BIN2. (A) Morphology of seedlings treated with mock or various salts. Seedlings were treated separately and arranged in a new plate to obtain a collective image of responses. First row, mock-treated control. Second row, treatment with KCl or LiCl alone. Third row, NaCl treatment in combination with KCl or LiCl. Scale bar = 5 mm. (B, C) Survival rate of Arabidopsis seedlings grown in 150 mM (B) or 200 mM NaCl media (C) supplemented with salts or bikinin (a BIN2 inhibitor). Survival rate was measured as the ratio of the number of green vs. pale yellow seedlings. Error bar = SD (n = 3). (D) GUS staining pattern in the roots of RD26pro:GUS seedlings. Scale bar = 1 mm.
Molecules and Cells 2014; 37: 795-803https://doi.org/10.14348/molcells.2014.0127

Fig 5.

Figure 5.Consensus sequence elements in the promoter of genes co-regulated by both ABA and BRs. The top fourmost over-represented motifs found in the -1000 bp proximal promoter of genes are shown. Genes that are (A) upregulated by ABA and downregulated by BR and (B) downregulated by ABA and upregulated by BR. Sequence logos for (A) and (B) were generated using the MEME analysis tool. The total information content of each logo is given in bits; the height of each nucleotide in the logo represents the positional probability of that nucleotide multiplied by the information content of the logo. E-value means the possibility of finding the motifs merely by chance.
Molecules and Cells 2014; 37: 795-803https://doi.org/10.14348/molcells.2014.0127

. Proportion of genes containing the BRRE.

ABABRsACCIAAGAMeJaCK
Up or DownUDUDUDUDUDUDUD
No. genes144014762683831673654303554082806701332163
BRRE-containing gene5243565913545871237811262721818146
BRRE/Total36.424.122.035.226.923.828.622.027.531.733.725.824.428.2

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Mol. Cells
Nov 30, 2022 Vol.45 No.11, pp. 763~867
COVER PICTURE
Naive (cyan) and axotomized (magenta) retinal ganglion cell axons in Xenopus tropicalis (Choi et al., pp. 846-854).

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